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Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their
concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and
other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can
easily spread and be consumed by humans.
Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.
Biodegradation is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through
different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as
the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is
defined as any metabolically-induced change in the chemical composition of a compound [14].
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation
processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in
situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade
a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive
and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and
other needs, to break down a contaminant. This is termed biostimulation. Biostimulation can be achieved through changes in pH, moisture,
aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed bioaugmentation,
where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not
mutually exclusive- they can be used simultaneously.
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily
degraded in the environment.
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms,
and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological
requirements, which are important in assessing the feasibility of bioremediation [4]. Biodegradability, or whether a chemical can be
degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread
these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its bioavailability, or
availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic
matter or trapped inside aggregates [4]. Physiological requirements, or set of conditions required by organisms to carry out bioremediation
in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the
environment needs to be habitable for organisms involved in bioremediation [4].
Contents
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1Brief History
2Overview of Pollutants
o 2.1Organic Pollutants
o 2.2Inorganic Pollutants
3Organisms
o 3.1Bacteria
3.1.1Pseudomonas putida
3.1.2Dechloromonas aromatica
3.1.3Nitrifiers and Denitrifiers
3.1.4Deinococcus radiodurans
3.1.5Methylibium petroleiphilum
3.1.6Alcanivorax borkumensis
o 3.2Fungi (Mycoremediation)
3.2.1Biodegradation Capacities of White rot fungi
3.2.2Phanerochaete chrysosporium
3.2.3Bioremediation of Hydrocarbon Pollutants
3.2.4Remediating Metals
3.2.5Pesticide Degradation
3.2.6Environmental Applications
o 3.3Archaea
3.3.1Examples of studies of Archaea involved in bioremediation
4Microbial Processes
o 4.1Factors Affecting Rates of Biodegradation
o 4.2Primary substrate utilization
o 4.3Cometabolism (Secondary Substrate Utilization)
o 4.4Reductive and Hydrolytic Dehalogenation
o 4.5Acclimation
o 4.6Detoxification and Activation
5Bioremediation treatment methods
o 5.1Ex-situ
5.1.1Biopiling
5.1.2Composting
o 5.2In-situ
5.2.1Biostimulation
5.2.2Metal Bioleaching
5.2.3Metal Biosorption
5.2.4Bioventing
o 5.3Ex-situ or In-situ
5.3.1Bioaugmentation
5.3.2Land Farming
5.3.3Biofilter
6Bioremediation Synopsis
o 6.1Advantages
o 6.2Disadvantages
7References
Brief History
Overview of Pollutants
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic
pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections. Below is a link to website
with a list of examples of soil pollutants and their effects on human health:
Summary of health effects of pollutants
Organic Pollutants
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic
pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are
highly toxic and they are associated with variety of health issues around the world [11].
Table below lists some groups of contaminants, examples, and their sources.
Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11].
The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.
Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6),
Inorganic Pollutants
Most inorganic pollutants are due to human activities.
Pollutant Source
Arsenic Pesticides, wood preservatives, biosolids, ore mining and smelting
Cadmium Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers
Chromium Tanneries, steel industries, fly ash
Copper Pesticides, fertilizers, biosolids, ore mining and smelting
Mercury Gold and Silver mining, coal combustion
Nickel Effluent, kitchen appliances, surgical instruments, automobile batteries
Lead Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.
A majority of heavy metal pollutants come from human sources that accumulate over time.
There are also natural forms of contamination from normal biological processes, which include:
1. Weathering of minerals over time
2. Erosion and volcanic activities
3. Forest fires and biogenic source
4. Particles released by vegetation
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals
through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates,
which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state
of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not
heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal
adsorption. Geomicrobiology takes a better look at the interactions between microbes and inorganic material.
Organisms
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental
pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of
bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated
artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon
and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation,
and archaea, the more recently discovered group of organisms with unique potential in bioremediation.
Bacteria
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal
toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic
versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in
bioremediation.
Pseudomonas putida
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is
also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]
Dechloromonas aromatica
Dechloromonas aromatica is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene,
coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to
the high propensity of benzene contamination, especially in ground and surface water, D. aromatic is especially useful for in situ
bioremediation of this substance. [13]
Deinococcus radiodurans
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents
and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive
mixed waste environments [7].
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like Paracoccus
denitrificans [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in
natural waters, are remediated.
Methylibium petroleiphilum
Methylibium petroleiphilum (formally known as PM1 strain) is a bacterium capable of methyl tert-butyl ether (MTBE) bioremediation. PM1
degrades MTBE by using the contaminant as the sole carbon and energy source [8].
Alcanivorax borkumensis
Alcanivorax borkumensis is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces
carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil
from the Deepwater Horizon oil spill in the Gulf of Mexico [25].
Fungi (Mycoremediation)
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally
important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic
materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and
reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental
resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and
high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile
species such as White Rot Fungi have been a hot topic of research. [16,17]
Phanerochaete chrysosporium
P. chrysosporium was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for
bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, P. chrysosporium has
become the model for bioremediation. Other notable species of white rot fungi include Pleurotus ostreatus and Trametes versicolor. [18]
Remediating Metals
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining
process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be
released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship
between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating
contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of
interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After
the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various
plants that participate in symbiosis. [17]
Pesticide Degradation
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water
supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient
because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a
potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high
promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This
fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]
Environmental Applications
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes.
Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their
highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because
of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in
situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and
bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]
Archaea
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers
have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in
bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.
- Biodegradation by extreme halophilic archaea was not recognized widely in the past, but scientists have found out that extreme halophilic
archaea have greater catabolic diversity than expected [9]
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low
temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and
bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important
degraders of hydrocarbons in those environments [10].
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in
bioremediation cannot survive or function properly. [5]
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them
great advantage in participating in bioremediation in the presence of antibiotics [5].
Microbial Processes
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon
and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the
diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are
described.
Acclimation
An acclimation period, also called an adaptation or lag period, occurs when no destruction of a given chemical is observed [23]. It is
caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere
from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending
on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and
concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few
consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl
parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound
dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as
phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe
human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it
can allow the substance to flow further and impact environments distant to its site of origin before being degraded.
A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain
circumstances [12]
Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]
Ex-situ
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12].
The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of
soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.
Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific
treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.
Biopiling
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and
blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may
affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated
soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation,
and volatilization.
Composting
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate
container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the
adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as
one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a
very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation
involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and
treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily
used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared
to quicker treatments such as biostimulation.
In-situ
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation,
bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-
situ, but it can be expensive due to specialized equipment.
Biostimulation
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading
microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron
acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or
activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of
nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that
are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily
available to the subsurface microbes.
Metal Bioleaching
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to
extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization.
Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains
(Aspergillus Niger, Penicillium Simplicissimum) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and
zinc[33], which will make them much easier to remove from the soil.
Metal Biosorption
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a
liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of
solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution
between the solid and liquid phases.
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is
primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption
technologies has been limited so far.
Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would
otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating
Bioventing
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in
the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the
coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier
hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.
Ex-situ or In-situ
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and
treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much
contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.
Bioaugmentation
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the
indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental
problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil
inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-
natives runs the possible risk of creating a monoculture in the soil.
Bioaugmentation is ideal for soil:
1. With low number of microbes that are capable of degrading targeted pollutants
2. Containing compounds requiring multi stepped remediation.
Augmentation techniques have a great potential for aromatic compound remediation. The most important step in successful
bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to
survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.
Land Farming
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into
lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it
is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is
uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material
is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as
allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil
conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions
that may be controlled [38].
The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]
Biofilter
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will
be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for
the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated
outflow of water. Chromobacterium violaceum, is used to treat water and soil contaminated with silver nanoparticles, reducing its
concentration.
Bioremediation Synopsis
Advantages
1. Bioremediation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize
contaminants increase in population when the contaminant is present. The inverse is true, degradation of the contaminant causes population
declines of those microbes. Usually the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]
2. Bioremediation is theoretically meant to completely degrade a wide range of pollutants into harmless products on site. This removes the
risks involved with transportation for treatment and elimination of contaminated substances. [12]
3. Bioremediation is meant to completely eliminate specific pollutants without the risks of transferring contaminants from one environmental
medium to another (land, air, water). [12]
4. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]
Disadvantages
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the
contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants
need to be met. [12]
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More
research needs to be completed to create technologies that can adapt. [12]
6. Compared to other treatment technologies, bioremediation often takes more time. [12]
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave
uncertainty in remediation dispersal